Variant report

Variant	rs6416258
Chromosome Location	chr12:9909997-9909998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:9907740..9910735-chr12:10101487..10103775,2	K562	blood:
2	chr12:9908727..9910946-chr12:9954413..9956000,2	K562	blood:
3	chr12:9514676..9517481-chr12:9908794..9910668,2	K562	blood:
4	chr12:9803491..9806822-chr12:9909601..9912697,3	K562	blood:
5	chr12:9909065..9911051-chr12:10072172..10073790,2	K562	blood:
6	chr12:9889267..9893240-chr12:9909352..9912451,4	K562	blood:
7	chr12:9909977..9913009-chr12:10364990..10367233,3	K562	blood:
8	chr12:9908521..9910612-chr12:10055343..10056923,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000256594	Chromatin interaction
ENSG00000139112	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1008611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10466762	1.00[JPT][hapmap]
rs1051065	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10743821	1.00[CHB][hapmap]
rs10743822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10772005	1.00[JPT][hapmap]
rs10772006	1.00[JPT][hapmap]
rs10772104	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10772119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844350	1.00[JPT][hapmap]
rs10844351	1.00[JPT][hapmap]
rs10844359	1.00[JPT][hapmap]
rs10844372	1.00[JPT][hapmap]
rs10844418	1.00[JPT][hapmap]
rs10844424	1.00[JPT][hapmap]
rs10844429	1.00[JPT][hapmap]
rs10844676	0.91[ASN][1000 genomes]
rs10844780	1.00[JPT][hapmap]
rs11052234	1.00[JPT][hapmap]
rs11052241	1.00[JPT][hapmap]
rs11052254	1.00[JPT][hapmap]
rs11052430	1.00[JPT][hapmap]
rs11052771	0.82[ASN][1000 genomes]
rs11053051	1.00[JPT][hapmap]
rs12366653	1.00[JPT][hapmap]
rs12368445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12578928	1.00[JPT][hapmap]
rs12810851	1.00[JPT][hapmap]
rs12823699	1.00[JPT][hapmap]
rs12824491	1.00[JPT][hapmap]
rs12825507	1.00[JPT][hapmap]
rs12828602	1.00[JPT][hapmap]
rs12830419	1.00[JPT][hapmap]
rs12831453	1.00[JPT][hapmap]
rs1560008	1.00[JPT][hapmap]
rs16913477	1.00[JPT][hapmap]
rs17806015	0.91[ASW][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1863871	1.00[JPT][hapmap]
rs1990533	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2114869	1.00[JPT][hapmap]
rs2114872	1.00[JPT][hapmap]
rs2401396	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2401397	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136577	0.81[ASN][1000 genomes]
rs3176793	0.91[ASW][hapmap];0.89[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs3176800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176804	0.81[ASN][1000 genomes]
rs3176806	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176807	0.81[ASN][1000 genomes]
rs3176808	0.81[ASN][1000 genomes]
rs34279883	0.81[ASN][1000 genomes]
rs35494990	0.81[ASN][1000 genomes]
rs4763299	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4763865	0.91[ASN][1000 genomes]
rs4763867	0.91[ASN][1000 genomes]
rs6488065	1.00[JPT][hapmap]
rs704223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132037	1.00[JPT][hapmap]
rs7297324	0.91[ASN][1000 genomes]
rs7302110	1.00[JPT][hapmap]
rs7302746	1.00[JPT][hapmap]
rs7304321	1.00[JPT][hapmap]
rs7304464	1.00[JPT][hapmap]
rs7309800	1.00[JPT][hapmap]
rs7310568	1.00[JPT][hapmap]
rs7310790	1.00[JPT][hapmap]
rs7310897	1.00[JPT][hapmap]
rs7311421	1.00[JPT][hapmap]
rs7311574	1.00[JPT][hapmap]
rs7311945	1.00[JPT][hapmap]
rs7312624	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7961416	1.00[JPT][hapmap]
rs7962321	1.00[JPT][hapmap]
rs7971721	0.91[ASN][1000 genomes]
rs7974871	1.00[JPT][hapmap]
rs7978187	1.00[JPT][hapmap]
rs929615	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9630265	1.00[JPT][hapmap]
rs982511	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9919786	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6416258	FOXJ2	cis	parietal	SCAN
rs6416258	KLRK1	cis	parietal	SCAN
rs6416258	TAS2R42	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9893400-9910800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:9896400-9911000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:9903400-9917600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:9903600-9911000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:9903800-9911200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:9904000-9910200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:9904200-9910800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:9904200-9911200	Weak transcription	Small Intestine	intestine
9	chr12:9904400-9913200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:9904600-9913400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
11	chr12:9905600-9913400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:9905800-9910600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:9907600-9910000	Genic enhancers	Dnd41	blood
14	chr12:9908200-9910200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:9908800-9910000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:9908800-9910600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:9909000-9914800	Active TSS	Thymus	Thymus
18	chr12:9909200-9910600	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr12:9909200-9911200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr12:9909400-9910600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:9909400-9911000	Active TSS	GM12878-XiMat	blood
22	chr12:9909600-9910000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:9909600-9910000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr12:9909600-9913400	Active TSS	Fetal Thymus	thymus
25	chr12:9909600-9914200	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr12:9909800-9910200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr12:9909800-9910200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr12:9909800-9910400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr12:9909800-9910600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr12:9909800-9910800	Enhancers	Primary B cells from peripheral blood	blood
31	chr12:9909800-9910800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
32	chr12:9909800-9910800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:9909800-9911400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
34	chr12:9909800-9911400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:9909800-9914000	Active TSS	K562	blood
36	chr12:9909800-9914400	Active TSS	Primary T cells fromperipheralblood	blood

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